Dear everybody: Packages that DO pass the package check on my Ubuntu 17.04 laptop with R 3.4.1 and Mac OSX do not build on Centos 7 with R 3.4.1. I'm pretty sure I have an environment defect, but cannot find it.
I find posts from various people about this problem since 2012. But I've checked the likely suspects. Among all the runs I pasted in below, the most informative error message I found is the very last one, which ends like this: It looks like this package has a loading problem when not on .libPaths: see the messages for details. The messages don't really help me understand (all pasted in full detail below), but I hope you'll say "aha", there's that environment thing again. I notice that package check proceeds differently without "--as-cran". In some cases, package check passes. Other times, it fails differently. Here are some details, I hope you have guesses about where to check for trouble. I suspected I had an error in my packages, so I picked some at random from the CRAN list, things which depend on openxlsx. It turns out they don't survive check either. Hopefully this makes it easy for you to replicate (copy/paste :) ) $ wget http://rweb.quant.ku.edu/cran/src/contrib/reproducer_0.1.9.tar.gz $ R CMD check --as-cran reproducer_0.1.9.tar.gz * using log directory ‘/tmp/pj/reproducer.Rcheck’ * using R version 3.4.1 (2017-06-30) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--as-cran’ * checking for file ‘reproducer/DESCRIPTION’ ... OK * this is package ‘reproducer’ version ‘0.1.9’ * checking CRAN incoming feasibility ... WARNING Maintainer: ‘Lech Madeyski <lech.madey...@gmail.com>’ Insufficient package version (submitted: 0.1.9, existing: 0.1.9) * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘reproducer’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... ERROR Running examples in ‘reproducer-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: boxplotAndDensityCurveOnHistogram > ### Title: boxplotAndDensityCurveOnHistogram > ### Aliases: boxplotAndDensityCurveOnHistogram > > ### ** Examples > > library(ggplot2) Error in library(ggplot2) : there is no package called ‘ggplot2’ Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) Error: package or namespace load failed for 'testthat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'R6' Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING See ‘/tmp/pj/reproducer.Rcheck/00check.log’ for details. Contents of 00check.log are same: The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: boxplotAndDensityCurveOnHistogram > ### Title: boxplotAndDensityCurveOnHistogram > ### Aliases: boxplotAndDensityCurveOnHistogram > > ### ** Examples > > library(ggplot2) Error in library(ggplot2) : there is no package called ‘ggplot2’ Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... ERROR Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) Error: package or namespace load failed for 'testthat' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called 'R6' Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 WARNING It says I'm missing packages, but not so! Observe a session: [pauljohn@crmda-026L pj]$ R R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(R6) > library(testthat) > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] testthat_1.0.2 R6_2.2.2 loaded via a namespace (and not attached): [1] compiler_3.4.1 magrittr_1.5 crayon_1.3.2 > Interestingly, if I run the check without "--as-cran", then there is no error and the check succeeds. Here's another package I chose at random. This one has exactly the same failure symptom that my packages do. $ wget http://rweb.quant.ku.edu/cran/src/contrib/tablaxlsx_1.2.2.tar.gz $ R CMD check --as-cran tablaxlsx_1.2.2.tar.gz * using log directory ‘/tmp/pj/tablaxlsx.Rcheck’ * using R version 3.4.1 (2017-06-30) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--as-cran’ * checking for file ‘tablaxlsx/DESCRIPTION’ ... OK * this is package ‘tablaxlsx’ version ‘1.2.2’ * package encoding: latin1 * checking CRAN incoming feasibility ... WARNING Maintainer: ‘Jesus Maria Rodriguez Rodriguez <jesus...@ono.com>’ Insufficient package version (submitted: 1.2.2, existing: 1.2.2) The Date field is over a month old. This build time stamp is over a month old. * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘tablaxlsx’ can be installed ... ERROR Installation failed. See ‘/tmp/pj/tablaxlsx.Rcheck/00install.out’ for details. * DONE Status: 1 ERROR, 1 WARNING See ‘/tmp/pj/tablaxlsx.Rcheck/00check.log’ for details. $ cat /tmp/pj/tablaxlsx.Rcheck/00install.out * installing *source* package ‘tablaxlsx’ ... ** package ‘tablaxlsx’ successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error: package or namespace load failed for ‘openxlsx’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Error : package ‘openxlsx’ could not be loaded Error: loading failed Execution halted ERROR: loading failed * removing ‘/tmp/pj/tablaxlsx.Rcheck/tablaxlsx’ But I do have Rcpp and openxlsx, could show you the session, as we did with testthat and R6 before. Moreover, observe I can install the package and it does load: $ R CMD INSTALL tablaxlsx_1.2.2.tar.gz * installing to library ‘/home/pauljohn/R/x86_64-redhat-linux-gnu-library/3.4’ * installing *source* package ‘tablaxlsx’ ... ** package ‘tablaxlsx’ successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices converting help for package ‘tablaxlsx’ finding HTML links ... done bordear html finding level-2 HTML links ... done escribirTabla html estilosDGE html estilosDGEPYE html reducir html tablaxlsx.estilos.set html trim html verXL html ** building package indices ** testing if installed package can be loaded * DONE (tablaxlsx) And, more importantly, the installed package will load: $ R R version 3.4.1 (2017-06-30) -- "Single Candle" Copyright (C) 2017 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(tablaxlsx) Loading required package: openxlsx > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] tablaxlsx_1.2.2 openxlsx_4.0.17 loaded via a namespace (and not attached): [1] compiler_3.4.1 Rcpp_0.12.12 Building this one without "--as-cran" results in a different/interesting error, it is more informative, but I don't understand it. $ R CMD check tablaxlsx_1.2.2.tar.gz * using log directory ‘/tmp/pj/tablaxlsx.Rcheck’ * using R version 3.4.1 (2017-06-30) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘tablaxlsx/DESCRIPTION’ ... OK * this is package ‘tablaxlsx’ version ‘1.2.2’ * package encoding: latin1 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘tablaxlsx’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... WARNING Loading required package: openxlsx Error: package or namespace load failed for ‘openxlsx’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘Rcpp’ Error: package ‘openxlsx’ could not be loaded Execution halted It looks like this package has a loading problem when not on .libPaths: see the messages for details. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... OK * checking PDF version of manual ... OK * DONE What does it mean? It is intriguing that we don't have this problem in Ubuntu or Macintosh. What other info you need? Inside R: > .libPaths() [1] "/home/pauljohn/R/x86_64-redhat-linux-gnu-library/3.4" [2] "/usr/lib64/R/library" [3] "/usr/share/R/library" The packages in question are all in "/usr/share/R/library". The system-wide R_LIBS_SITE has that directory, Local Variables of /usr/lib64/R/etc/Renviron: R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib64/R/library:/usr/share/R/library'} I have no folder named ~/.R Thanks in advance, friends. pj -- Paul E. Johnson http://pj.freefaculty.org Director, Center for Research Methods and Data Analysis http://crmda.ku.edu To write to me directly, please address me at pauljohn at ku.edu. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.